Generic.py

# Copyright 2000-2004 Brad Chapman.# Copyright 2001 Iddo Friedberg.# Copyright 2007-2010 by Peter Cock.# All rights reserved.# This code is part of the Biopython distribution and governed by its# license. Please see the LICENSE file that should have been included# as part of this package."""Contains classes to deal with generic sequence alignment stuff notspecific to a particular program or format.classes:o Alignment"""# biopythonfrom Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import Alphabet
00021class Alignment:
"""Represent a set of alignments (OBSOLETE?). This is a base class to represent alignments, which can be subclassed to deal with an alignment in a specific format. With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is effectively obsolete and will likely be deprecated and later removed in future releases of Biopython. """00031def __init__(self, alphabet):
"""Initialize a new Alignment object. Arguments: o alphabet - The alphabet to use for the sequence objects that are created. This alphabet must be a gapped type. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma """import warnings
warnings.warn("With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is effectively obsolete and will likely be deprecated and later removed in future releases of Biopython.", PendingDeprecationWarning)
ifnot (isinstance(alphabet, Alphabet.Alphabet) \
or isinstance(alphabet, Alphabet.AlphabetEncoder)):
raise ValueError("Invalid alphabet argument")
self._alphabet = alphabet
# hold everything at a list of SeqRecord objects
self._records = []
00059def _str_line(self, record):
"""Returns a truncated string representation of a SeqRecord (PRIVATE). This is a PRIVATE function used by the __str__ method. """if len(record.seq) <= 50:
return"%s %s" % (record.seq, record.id)
else:
return"%s...%s %s" \
% (record.seq[:44], record.seq[-3:], record.id)
00070def __str__(self):
"""Returns a multi-line string summary of the alignment. This output is intended to be readable, but large alignments are shown truncated. A maximum of 20 rows (sequences) and 50 columns are shown, with the record identifiers. This should fit nicely on a single screen. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACT-CTAGCTAG Beta ACTGCTAGATAG Gamma See also the alignment's format method. """
rows = len(self._records)
lines = ["%s alignment with %i rows and %i columns" \
% (str(self._alphabet), rows, self.get_alignment_length())]
if rows <= 20:
lines.extend([self._str_line(rec) for rec in self._records])
else:
lines.extend([self._str_line(rec) for rec in self._records[:18]])
lines.append("...")
lines.append(self._str_line(self._records[-1]))
return"\n".join(lines)
00102def __repr__(self):
"""Returns a representation of the object for debugging. The representation cannot be used with eval() to recreate the object, which is usually possible with simple python ojects. For example: <Bio.Align.Generic.Alignment instance (2 records of length 14, SingleLetterAlphabet()) at a3c184c> The hex string is the memory address of the object, see help(id). This provides a simple way to visually distinguish alignments of the same size. """#A doctest for __repr__ would be nice, but __class__ comes out differently#if run via the __main__ trick.return"<%s instance (%i records of length %i, %s) at %x>" % \
(self.__class__, len(self._records),
self.get_alignment_length(), repr(self._alphabet), id(self))
#This version is useful for doing eval(repr(alignment)),#but it can be VERY long:#return "%s(%s, %s)" \# % (self.__class__, repr(self._records), repr(self._alphabet))00125def format(self, format):
"""Returns the alignment as a string in the specified file format. The format should be a lower case string supported as an output format by Bio.AlignIO (such as "fasta", "clustal", "phylip", "stockholm", etc), which is used to turn the alignment into a string. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> print align.format("fasta") >Alpha ACTGCTAGCTAG >Beta ACT-CTAGCTAG >Gamma ACTGCTAGATAG <BLANKLINE> >>> print align.format("phylip") 3 12 Alpha ACTGCTAGCT AG Beta ACT-CTAGCT AG Gamma ACTGCTAGAT AG <BLANKLINE> For Python 2.6, 3.0 or later see also the built in format() function. """#See also the __format__ added for Python 2.6 / 3.0, PEP 3101#See also the SeqRecord class and its format() method using Bio.SeqIOreturn self.__format__(format)
00161def __format__(self, format_spec):
"""Returns the alignment as a string in the specified file format. This method supports the python format() function added in Python 2.6/3.0. The format_spec should be a lower case string supported by Bio.AlignIO as an output file format. See also the alignment's format() method."""if format_spec:
from StringIO import StringIO
from Bio import AlignIO
handle = StringIO()
AlignIO.write([self], handle, format_spec)
return handle.getvalue()
else:
#Follow python convention and default to using __str__return str(self)
00178def get_all_seqs(self):
"""Return all of the sequences involved in the alignment (DEPRECATED). The return value is a list of SeqRecord objects. This method is deprecated, as the Alignment object itself now offers much of the functionality of a list of SeqRecord objects (e.g. iteration or slicing to create a sub-alignment). Instead use the Python builtin function list, i.e. my_list = list(my_align) """import warnings
import Bio
warnings.warn("This method is deprecated, since the alignment object""now acts more like a list. Instead of calling ""align.get_all_seqs() you can use list(align)",
Bio.BiopythonDeprecationWarning)
return self._records00196def __iter__(self):
"""Iterate over alignment rows as SeqRecord objects. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> for record in align: ... print record.id ... print record.seq Alpha ACTGCTAGCTAG Beta ACT-CTAGCTAG Gamma ACTGCTAGATAG """return iter(self._records)
00217def get_seq_by_num(self, number):
"""Retrieve a sequence by row number (OBSOLETE). Returns: o A Seq object for the requested sequence. Raises: o IndexError - If the specified number is out of range. NOTE: This is a legacy method. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects. e.g. for record in alignment: print record.id print record.seq first_record = alignment[0] last_record = alignment[-1] """import warnings
warnings.warn("This is a legacy method. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects.", PendingDeprecationWarning)
return self._records[number].seq
00240def __len__(self):
"""Returns the number of sequences in the alignment. Use len(alignment) to get the number of sequences (i.e. the number of rows), and alignment.get_alignment_length() to get the length of the longest sequence (i.e. the number of columns). This is easy to remember if you think of the alignment as being like a list of SeqRecord objects. """return len(self._records)
00252def get_alignment_length(self):
"""Return the maximum length of the alignment. All objects in the alignment should (hopefully) have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.get_alignment_length() 12 If you want to know the number of sequences in the alignment, use len(align) instead: >>> len(align) 3 """
max_length = 0
for record in self._records:
if len(record.seq) > max_length:
max_length = len(record.seq)
return max_length
00282def add_sequence(self, descriptor, sequence, start = None, end = None,
weight = 1.0):
"""Add a sequence to the alignment. This doesn't do any kind of alignment, it just adds in the sequence object, which is assumed to be prealigned with the existing sequences. Arguments: o descriptor - The descriptive id of the sequence being added. This will be used as the resulting SeqRecord's .id property (and, for historical compatibility, also the .description property) o sequence - A string with sequence info. o start - You can explicitly set the start point of the sequence. This is useful (at least) for BLAST alignments, which can just be partial alignments of sequences. o end - Specify the end of the sequence, which is important for the same reason as the start. o weight - The weight to place on the sequence in the alignment. By default, all sequences have the same weight. (0.0 => no weight, 1.0 => highest weight) """
new_seq = Seq(sequence, self._alphabet)
#We are now effectively using the SeqRecord's .id as#the primary identifier (e.g. in Bio.SeqIO) so we should#populate it with the descriptor.#For backwards compatibility, also store this in the#SeqRecord's description property.
new_record = SeqRecord(new_seq,
id = descriptor,
description = descriptor)
# hack! We really need to work out how to deal with annotations# and features in biopython. Right now, I'll just use the# generic annotations dictionary we've got to store the start# and end, but we should think up something better. I don't know# if I'm really a big fan of the LocatableSeq thing they've got# in BioPerl, but I'm not positive what the best thing to do on# this is...if start:
new_record.annotations['start'] = start
if end:
new_record.annotations['end'] = end
# another hack to add weight information to the sequence
new_record.annotations['weight'] = weight
self._records.append(new_record)
00333def get_column(self,col):
"""Returns a string containing a given column. e.g. >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.get_column(0) 'AAA' >>> align.get_column(3) 'G-G' """#TODO - Support negative indices?
col_str = ''assert col >= 0 and col <= self.get_alignment_length()
for rec in self._records:
col_str += rec.seq[col]
return col_str
00354def __getitem__(self, index):
"""Access part of the alignment. We'll use the following example alignment here for illustration: >>> from Bio.Alphabet import IUPAC, Gapped >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-")) >>> align.add_sequence("Alpha", "ACTGCTAGCTAG") >>> align.add_sequence("Beta", "ACT-CTAGCTAG") >>> align.add_sequence("Gamma", "ACTGCTAGATAG") >>> align.add_sequence("Delta", "ACTGCTTGCTAG") >>> align.add_sequence("Epsilon","ACTGCTTGATAG") You can access a row of the alignment as a SeqRecord using an integer index (think of the alignment as a list of SeqRecord objects here): >>> first_record = align[0] >>> print first_record.id, first_record.seq Alpha ACTGCTAGCTAG >>> last_record = align[-1] >>> print last_record.id, last_record.seq Epsilon ACTGCTTGATAG You can also access use python's slice notation to create a sub-alignment containing only some of the SeqRecord objects: >>> sub_alignment = align[2:5] >>> print sub_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGATAG Gamma ACTGCTTGCTAG Delta ACTGCTTGATAG Epsilon This includes support for a step, i.e. align[start:end:step], which can be used to select every second sequence: >>> sub_alignment = align[::2] >>> print sub_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns ACTGCTAGCTAG Alpha ACTGCTAGATAG Gamma ACTGCTTGATAG Epsilon Or to get a copy of the alignment with the rows in reverse order: >>> rev_alignment = align[::-1] >>> print rev_alignment Gapped(IUPACUnambiguousDNA(), '-') alignment with 5 rows and 12 columns ACTGCTTGATAG Epsilon ACTGCTTGCTAG Delta ACTGCTAGATAG Gamma ACT-CTAGCTAG Beta ACTGCTAGCTAG Alpha Right now, these are the ONLY indexing operations supported. The use of a second column based index is under discussion for a future update. """if isinstance(index, int):
#e.g. result = align[x]#Return a SeqRecordreturn self._records[index]
elif isinstance(index, slice):
#e.g. sub_aling = align[i:j:k]#Return a new Alignment using only the specified records.#TODO - See Bug 2554 for changing the __init__ method#to allow us to do this more cleanly.
sub_align = Alignment(self._alphabet)
sub_align._records = self._records[index]
return sub_align
elif len(index)==2:
raise TypeError("Row and Column indexing is not currently supported,"\
+"but may be in future.")
else:
raise TypeError("Invalid index type.")
def _test():
"""Run the Bio.Align.Generic module's doctests."""print"Running doctests..."import doctest
doctest.testmod()
print"Done"if __name__ == "__main__":
_test()